varona.bcftools

Module specifically for using (non-pysam) bcftools.

ALLOWED_TAGS = {'AC', 'AF', 'AN', 'MAF'}

Set of allowed tags that can be added to the VCF file.

HAVE_BCFTOOLS = False

True if the bcftools command is available on the system.

Regardless of whether the bcftools command can be found, this variable will be set to False if the environment variable VARONA_DISABLE_BCFTOOLS is set to “1”.

class VariantFileFilledInTags(filename, _, fillin_tags: list[str], *args, **kwargs)[source]

Bases: VariantFile

A subclass of pysam.VariantFile that fills in tags using bcftools.

It’ll preprocess the original VCF before opening the processed VCF. The

Parameters:

  • filename – Path to the VCF file.

  • _ – Ignored mode parameter (always “r” for read-only mode).

  • fillin_tags – List of tags to fill in the VCF file.

  • args – Additional arguments to pass to pysam.VariantFile.

  • kwargs – Additional keyword arguments to pass to pysam.VariantFile.

Raises:

RuntimeError – If bcftools isn’t available on the path.

close(self)[source]

closes the pysam.VariantFile.

run_bcftools_fill_tags(input_vcf: Path, output_vcf: Path, tags: list[str]) → None[source]

Run the bcftools fill-tags plugin to add AN, AC, AF, and MAF tags.

Parameters:

  • input_vcf – Path to the input VCF file (compressed with bgzip).

  • output_vcf – Path to the output VCF file (compressed with bgzip).

  • tags – List of tags to add to the VCF file can be any of AN, AC, AF, MAF.

Raises:

subprocess.CalledProcessError – If the bcftools command fails.